Name: Lysobacter tolerans UM1
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 132485

Type strain:

Species: Lysobacter tolerans

Strain Designation: UM1

Culture col. no.: DSM 28473, KCTC 42936, MCC 2572

Strain history: <- R. Lal, Univ. Delhi, Dept. Zoology; UM <- U. Mukherjee, Univ. Delhi, Dept. Zoology, India

NCBI tax ID(s): 1604334 (species)

Section

Lysobacter tolerans UM1 is an aerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from soil from hexachlorocyclohexane-contaminated dumpsite.

colony-forming
Gram-negative
rod-shaped
aerobe
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Gammaproteobacteria*
	Order	*Lysobacterales*
	Family	*Lysobacteraceae*
	Genus	*Lysobacter*
	Species	**Lysobacter tolerans**
	Full Scientific Name (LPSN)	Lysobacter tolerans (Rani et al. 2016) Margesin et al. 2018

Synonym

Luteimonas tolerans

Information on morphological and physiological properties Morphology

[Ref.: #43676]	Gram stain	negative

[Ref.: #43676]	Cell shape	rod-shaped

[Ref.: #43676]	Motility	no

[Ref.: #43676]	Colony color	Yellow
[Ref.: #43676]	Colony shape	circular
[Ref.: #43676]	Cultivation medium used	Luria Bertani agar

Multimedia content

[Ref.: #24274]

Intellectual property rights:

Information on culture and growth conditions Culture and growth conditions

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Culture medium

LB (Luria-Bertani) MEDIUM

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Culture medium growth

	Temperatures	Kind of temperature		Temperature
[Ref.: #43676]			growth	25-40 °C
[Ref.: #43676]			optimum	28 °C

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Temperature range

mesophilic

	pH	Kind of pH		pH
[Ref.: #43676]			optimum	8
[Ref.: #43676]			growth	3-10

Information on physiology and metabolism Physiology and metabolism

[Ref.: #43676]

Oxygen tolerance

aerobe

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Ability of spore formation

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #43676]		NaCl		growth	0-1	%(w/v)

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #43676]	D-fructose ChEBI	+	assimilation
[Ref.: #43676]	D-fructose ChEBI	+	carbon source
[Ref.: #43676]	D-galactose ChEBI	-	carbon source
[Ref.: #43676]	D-glucose ChEBI	+	assimilation
[Ref.: #43676]	D-glucose ChEBI	+	carbon source
[Ref.: #43676]	esculin ChEBI	-	hydrolysis
[Ref.: #43676]	gelatin ChEBI	-	hydrolysis
[Ref.: #43676]	nitrate ChEBI	-	reduction
[Ref.: #43676]	urea ChEBI	-	hydrolysis

	Metabolite	Antibiotic resistance
[Ref.: #43676]	ampicillin ChEBI	yes
[Ref.: #43676]	penicillin ChEBI	yes
[Ref.: #43676]	rifampicin ChEBI	yes

	Enzyme	Enzyme activity	EC number
[Ref.: #43676]	beta-galactosidase	-	3.2.1.23
[Ref.: #43676]	catalase	+	1.11.1.6
[Ref.: #43676]	cytochrome oxidase	+	1.9.3.1

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #43676]

Fatty acid	Percentage
C15:0 iso	36
C17:0 iso 3OH	15
C15:1 iso G	14.9
C16:1ω7c / C16:1ω6c	12.1
C16:0-10-methyl / iso-C17:1ω9c	9.2
C15:0 iso 3OH	4.4
C17:1 iso I / C17:1 anteiso B	1.6
C16:0	1.6
C14:0	1
C15:0 anteiso	1

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	cyanate degradation	100	3 of 3
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	palmitate biosynthesis	95.45	21 of 22
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	serine metabolism	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	tetrahydrofolate metabolism	85.71	12 of 14
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	methylglyoxal degradation	80	4 of 5
[Ref.: #66794]	propionate fermentation	80	8 of 10
[Ref.: #66794]	peptidoglycan biosynthesis	80	12 of 15
[Ref.: #66794]	photosynthesis	78.57	11 of 14
[Ref.: #66794]	heme metabolism	78.57	11 of 14
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	NAD metabolism	77.78	14 of 18
[Ref.: #66794]	phenylalanine metabolism	76.92	10 of 13
[Ref.: #66794]	vitamin B1 metabolism	76.92	10 of 13
[Ref.: #66794]	purine metabolism	76.6	72 of 94
[Ref.: #66794]	acetate fermentation	75	3 of 4
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	gluconeogenesis	75	6 of 8
[Ref.: #66794]	pentose phosphate pathway	72.73	8 of 11
[Ref.: #66794]	cardiolipin biosynthesis	71.43	5 of 7
[Ref.: #66794]	ubiquinone biosynthesis	71.43	5 of 7
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tryptophan metabolism	71.05	27 of 38
[Ref.: #66794]	lipid metabolism	70.97	22 of 31
[Ref.: #66794]	threonine metabolism	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	alanine metabolism	68.97	20 of 29
[Ref.: #66794]	glutamate and glutamine metabolism	67.86	19 of 28
[Ref.: #66794]	octane oxidation	66.67	2 of 3
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	IAA biosynthesis	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	flavin biosynthesis	66.67	10 of 15
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	62.5	5 of 8
[Ref.: #66794]	starch degradation	60	6 of 10
[Ref.: #66794]	D-cycloserine biosynthesis	60	3 of 5
[Ref.: #66794]	lipoate biosynthesis	60	3 of 5
[Ref.: #66794]	propanol degradation	57.14	4 of 7
[Ref.: #66794]	glutathione metabolism	57.14	8 of 14
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	cysteine metabolism	55.56	10 of 18
[Ref.: #66794]	d-mannose degradation	55.56	5 of 9
[Ref.: #66794]	non-pathway related	55.26	21 of 38
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	isoprenoid biosynthesis	53.85	14 of 26
[Ref.: #66794]	quinate degradation	50	1 of 2
[Ref.: #66794]	isoleucine metabolism	50	4 of 8
[Ref.: #66794]	dTDPLrhamnose biosynthesis	50	4 of 8
[Ref.: #66794]	cis-vaccenate biosynthesis	50	1 of 2
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	dolichol and dolichyl phosphate biosynthesis	50	1 of 2
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	phenylmercury acetate degradation	50	1 of 2
[Ref.: #66794]	coenzyme A metabolism	50	2 of 4
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	50	6 of 12
[Ref.: #66794]	glycogen biosynthesis	50	2 of 4
[Ref.: #66794]	ribulose monophosphate pathway	50	1 of 2
[Ref.: #66794]	sulfate reduction	46.15	6 of 13
[Ref.: #66794]	proline metabolism	45.45	5 of 11
[Ref.: #66794]	valine metabolism	44.44	4 of 9
[Ref.: #66794]	reductive acetyl coenzyme A pathway	42.86	3 of 7
[Ref.: #66794]	tyrosine metabolism	42.86	6 of 14
[Ref.: #66794]	vitamin K metabolism	40	2 of 5
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	urea cycle	38.46	5 of 13
[Ref.: #66794]	degradation of sugar alcohols	37.5	6 of 16
[Ref.: #66794]	ketogluconate metabolism	37.5	3 of 8
[Ref.: #66794]	oxidative phosphorylation	36.26	33 of 91
[Ref.: #66794]	polyamine pathway	34.78	8 of 23
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	sphingosine metabolism	33.33	2 of 6
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	phenylpropanoid biosynthesis	30.77	4 of 13
[Ref.: #66794]	coenzyme M biosynthesis	30	3 of 10
[Ref.: #66794]	degradation of hexoses	27.78	5 of 18
[Ref.: #66794]	metabolism of disaccharids	27.27	3 of 11
[Ref.: #66794]	ascorbate metabolism	27.27	6 of 22
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cholesterol biosynthesis	27.27	3 of 11
[Ref.: #66794]	3-phenylpropionate degradation	26.67	4 of 15
[Ref.: #66794]	lactate fermentation	25	1 of 4
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	toluene degradation	25	1 of 4
[Ref.: #66794]	vitamin E metabolism	25	1 of 4
[Ref.: #66794]	catecholamine biosynthesis	25	1 of 4
[Ref.: #66794]	degradation of pentoses	25	7 of 28
[Ref.: #66794]	carnitine metabolism	25	2 of 8
[Ref.: #66794]	nitrate assimilation	22.22	2 of 9
		Only first 10 entries are displayed. Click here to see all.

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #24274]	Sample type/isolated from	soil from hexachlorocyclohexane-contaminated dumpsite
[Ref.: #24274]	Geographic location (country and/or sea, region)	Lucknow, Ummari village
[Ref.: #24274]	Country	India
[Ref.: #24274]	Country ISO 3 Code	IND
[Ref.: #24274]	Continent	Asia

[Ref.: #43676]	Sample type/isolated from	hexachlorocyclohexane-contaminated dumpsite in Ummari village
[Ref.: #43676]	Geographic location (country and/or sea, region)	Lucknow
[Ref.: #43676]	Country	India
[Ref.: #43676]	Country ISO 3 Code	IND
[Ref.: #43676]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Terrestrial	#Soil
#Engineered	#Contamination	-
#Engineered	#Waste	-

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence KM888877 (>99% sequence identity) for Lysobacter tolerans subclade from Microbeatlas

Aquatic Samples	686
Soil Samples	139
Animal Samples	601
Plant Samples	47
Total Samples	1473

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #24274]	Luteimonas tolerans strain UM1 16S ribosomal RNA gene, partial sequence	KM888877	1419	ENA	1604334 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Lysobacter tolerans UM1	GCA_900155935	contig	GenBank	1604334 tax ID	*
[Ref.: #66792]	Lysobacter tolerans UM1	2681812867	draft	JGI IMG/M	1604334 tax ID	*

[Ref.: #43676]	GC-content	64.3 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #24274]	GC-content	64.3 mol%	fluorimetric

Availability in culture collections External links

[Ref.: #24274]

Culture collection no.

DSM 28473, KCTC 42936, MCC 2572

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Proposal of Lysobacter pythonis sp. nov. isolated from royal pythons (Python regius).	Busse HJ, Huptas C, Baumgardt S, Loncaric I, Spergser J, Scherer S, Wenning M, Kampfer P	Syst Appl Microbiol	10.1016/j.syapm.2019.02.002	2019	*
Phylogeny	Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil.	Rani P, Mukherjee U, Verma H, Kamra K, Lal R	Int J Syst Evol Microbiol	10.1099/ijsem.0.000956	2016	*

References

#20215

Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#24274

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 28473

#43676

Pooja Rani, Udita Mukherjee, Helianthous Verma, Komal Kamra, Rup Lal: Luteimonas tolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. IJSEM 66: 1851 - 1856 2016 ( DOI 10.1099/ijsem.0.000956 , PubMed 26869334 )

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

#69479

João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .

* These data were automatically processed and therefore are not curated

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